I have a couple:
The Punisher. It's never going to be made right, but it would be awesome to make an M rated cartoon like the Spawn one HBO had.
InFAMOUS would make for an interesting series. Basically, for the series, it would be an alternate universe where Cole does not order the Armageddon special and opted for a middle option where Conduits are activated but not at the cost all the Humans, one that the game could not give you. Moral Choice and All that.
A Boy and His Blob would make for an excellent 65 episode series. Its simple premise needs to be expanded on a little bit, but it could work. Add about 14-20 more people in that world, put in a few more aliens bad guys, ones that do not have Blob's limitations, and .
Also, I have a few that I want to see new seasons:
Gargoyles. Not really interested in the 1994 storyline because it is fairly complete, but expand other concepts in that universe. In addition to the three that Greg Weissman wanted to do, 2198, Medieval, and Brooklyn being Lost in Time, there are so many ways the story can go. After Goliath, Bronx, Angela, and Elisa left Avalon, they went through a lot of places that were essentially spin off fodder. CulChulain, Dingo, New Olympians, Sentinel, and the two panthers in Africa could easily have 65 episode series, especially considering that the Pack, Xanatos, and Oberon's Children, are still around. Beyond that, there is that whole Illuminati storyline still floating around.
Wolverine and the X-Men could have had a few more seasons beyond the Age of Apocalypse storyline. Old Man Logan might work, as well as a Here Comes Tomorrow storyline. Beyond that there might be one where the Brood took over, one cause by that sentient virus John Wraith, and a few that I can't even think of. It would have been fun.